Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forgev0.9-39

7 files changed, 53 insertions, 51 deletions

diff --git a/README.Rmd b/README.Rmd
index e7cc5798..a3d191d1 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -154,7 +154,8 @@ for installation instructions and a manual.
   
 ## News
 
-Yes, there is a ![Changelog](NEWS.md).
+Yes, there is a ChangeLog, for the latest [CRAN release](http://cran.r-project.org/web/packages/mkin/NEWS.html)
+and one for the [github master branch](https://github.com/jranke/mkin/blob/master/NEWS.md).
 
 ## Credits and historical remarks
 
diff --git a/README.md b/README.md
index 259a73a3..50fc4412 100644
--- a/README.md
+++ b/README.md
@@ -168,7 +168,8 @@ for installation instructions and a manual.
   
 ## News
 
-Yes, there is a ![Changelog](https://github.com/jranke/mkin/blob/master/NEWS.md).
+Yes, there is a ChangeLog, for the latest [CRAN release](http://cran.r-project.org/web/packages/mkin/NEWS.html)
+and one for the [github master branch](https://github.com/jranke/mkin/blob/master/NEWS.md).
 
 ## Credits and historical remarks
 
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index 6b4d8b95..b8264c22 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -137,8 +137,8 @@ print(FOCUS_2006_D)</code></pre>
 <pre class="r"><code>summary(fit)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:46 2015 
-## Date of summary: Fri Jun 26 16:06:47 2015 
+## Date of fit:     Fri Jun 26 16:35:59 2015 
+## Date of summary: Fri Jun 26 16:35:59 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)</code></pre>
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.741 s
+## Fitted with method Port using 153 model solutions performed in 0.71 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 7fb65960..d1a10e6a 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -93,15 +93,15 @@ FOCUS_2006_L1_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L1)</code></pre>
 summary(m.L1.SFO)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:47 2015 
-## Date of summary: Fri Jun 26 16:06:47 2015 
+## Date of fit:     Fri Jun 26 16:36:00 2015 
+## Date of summary: Fri Jun 26 16:36:00 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.096 s
+## Fitted with method Port using 37 model solutions performed in 0.095 s
 ## 
 ## Weighting: none
 ## 
@@ -183,8 +183,8 @@ summary(m.L1.SFO)</code></pre>
 <pre class="r"><code>summary(m.L1.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:48 2015 
-## Date of summary: Fri Jun 26 16:06:48 2015 
+## Date of fit:     Fri Jun 26 16:36:00 2015 
+## Date of summary: Fri Jun 26 16:36:00 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 0.555 s
+## Fitted with method Port using 188 model solutions performed in 0.48 s
 ## 
 ## Weighting: none
 ## 
@@ -263,15 +263,15 @@ FOCUS_2006_L2_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L2)</code></pre>
 summary(m.L2.SFO)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:48 2015 
-## Date of summary: Fri Jun 26 16:06:48 2015 
+## Date of fit:     Fri Jun 26 16:36:01 2015 
+## Date of summary: Fri Jun 26 16:36:01 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.112 s
+## Fitted with method Port using 41 model solutions performed in 0.103 s
 ## 
 ## Weighting: none
 ## 
@@ -351,15 +351,15 @@ mkinresplot(m.L2.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L2.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:49 2015 
-## Date of summary: Fri Jun 26 16:06:49 2015 
+## Date of fit:     Fri Jun 26 16:36:01 2015 
+## Date of summary: Fri Jun 26 16:36:01 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.21 s
+## Fitted with method Port using 81 model solutions performed in 0.212 s
 ## 
 ## Weighting: none
 ## 
@@ -423,8 +423,8 @@ plot(m.L2.DFOP)</code></pre>
 <pre class="r"><code>summary(m.L2.DFOP, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:52 2015 
-## Date of summary: Fri Jun 26 16:06:52 2015 
+## Date of fit:     Fri Jun 26 16:36:03 2015 
+## Date of summary: Fri Jun 26 16:36:03 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.945 s
+## Fitted with method Port using 336 model solutions performed in 0.862 s
 ## 
 ## Weighting: none
 ## 
@@ -500,15 +500,15 @@ plot(m.L3.SFO)</code></pre>
 <pre class="r"><code>summary(m.L3.SFO)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:52 2015 
-## Date of summary: Fri Jun 26 16:06:52 2015 
+## Date of fit:     Fri Jun 26 16:36:04 2015 
+## Date of summary: Fri Jun 26 16:36:04 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.122 s
+## Fitted with method Port using 43 model solutions performed in 0.103 s
 ## 
 ## Weighting: none
 ## 
@@ -576,15 +576,15 @@ plot(m.L3.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L3.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:52 2015 
-## Date of summary: Fri Jun 26 16:06:52 2015 
+## Date of fit:     Fri Jun 26 16:36:04 2015 
+## Date of summary: Fri Jun 26 16:36:04 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.235 s
+## Fitted with method Port using 83 model solutions performed in 0.205 s
 ## 
 ## Weighting: none
 ## 
@@ -642,8 +642,8 @@ plot(m.L3.DFOP)</code></pre>
 <pre class="r"><code>summary(m.L3.DFOP, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:53 2015 
-## Date of summary: Fri Jun 26 16:06:53 2015 
+## Date of fit:     Fri Jun 26 16:36:05 2015 
+## Date of summary: Fri Jun 26 16:36:05 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.385 s
+## Fitted with method Port using 137 model solutions performed in 0.361 s
 ## 
 ## Weighting: none
 ## 
@@ -724,15 +724,15 @@ plot(m.L4.SFO)</code></pre>
 <pre class="r"><code>summary(m.L4.SFO, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:53 2015 
-## Date of summary: Fri Jun 26 16:06:53 2015 
+## Date of fit:     Fri Jun 26 16:36:05 2015 
+## Date of summary: Fri Jun 26 16:36:05 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.116 s
+## Fitted with method Port using 46 model solutions performed in 0.11 s
 ## 
 ## Weighting: none
 ## 
@@ -789,15 +789,15 @@ plot(m.L4.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L4.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:06:54 2015 
-## Date of summary: Fri Jun 26 16:06:54 2015 
+## Date of fit:     Fri Jun 26 16:36:05 2015 
+## Date of summary: Fri Jun 26 16:36:05 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.175 s
+## Fitted with method Port using 66 model solutions performed in 0.174 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 3245544c..8b8f7416 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index a62f3826..a8f6e3ef 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -99,18 +99,18 @@ smb.1 &lt;- summary(mb.1)[-1]
 rownames(smb.1) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;Eigenvalue based&quot;, &quot;deSolve, compiled&quot;)
 print(smb.1)</code></pre>
 <pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 7047.6039 7083.3201 7123.5962 7119.0364 7161.5924
-## Eigenvalue based       901.5593  924.3357  968.8689  947.1121 1002.5238
-## deSolve, compiled      765.7604  770.7657  786.8638  775.7709  797.4156
+## deSolve, not compiled 6767.3728 6834.5128 6879.5969 6901.6528 6935.7090
+## Eigenvalue based       977.5545 1161.8591 1225.1262 1346.1637 1348.9120
+## deSolve, compiled      761.0689  761.8958  772.3379  762.7228  777.9724
 ##                             max neval
-## deSolve, not compiled 7204.1483     3
-## Eigenvalue based      1057.9355     3
-## deSolve, compiled      819.0602     3</code></pre>
-<p>We see that using the compiled model is by a factor of 9.2 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
+## deSolve, not compiled 6969.7653     3
+## Eigenvalue based      1351.6603     3
+## deSolve, compiled      793.2221     3</code></pre>
+<p>We see that using the compiled model is by a factor of 9 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
 <pre class="r"><code>smb.1[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                         median
-## deSolve, not compiled 9.176725
-## Eigenvalue based      1.220866
+## deSolve, not compiled 9.048704
+## Eigenvalue based      1.764945
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -128,16 +128,16 @@ smb.2 &lt;- summary(mb.2)[-1]
 rownames(smb.2) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;deSolve, compiled&quot;)
 print(smb.2)</code></pre>
 <pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 14.080456 14.209689 14.287313 14.338922 14.390742
-## deSolve, compiled      1.467266  1.521451  1.555168  1.575636  1.599119
+## deSolve, not compiled 14.161917 14.189080 14.201763 14.216243 14.221687
+## deSolve, compiled      1.358691  1.366613  1.393306  1.374535  1.410614
 ##                             max neval
-## deSolve, not compiled 14.442561     3
-## deSolve, compiled      1.622601     3</code></pre>
+## deSolve, not compiled 14.227131     3
+## deSolve, compiled      1.446693     3</code></pre>
 <pre class="r"><code>smb.2[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                         median
-## deSolve, not compiled 9.100402
-## deSolve, compiled     1.000000</code></pre>
-<p>Here we get a performance benefit of a factor of 9.1 using the version of the differential equation model compiled from C code using the inline package!</p>
+## deSolve, not compiled 10.34258
+## deSolve, compiled      1.00000</code></pre>
+<p>Here we get a performance benefit of a factor of 10.3 using the version of the differential equation model compiled from C code using the inline package!</p>
 <p>This vignette was built with mkin 0.9.39 on</p>
 <pre><code>## R version 3.2.1 (2015-06-18)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 76426c30..4eb5dada 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf